MCB 150 Exam II Review

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Overall equation for cellular respiration

C6H12O6 + 6O2 → 6CO2 + 6H2O + ATP. Glucose is broken down into carbon dioxide and water, releasing energy in the form of ATP.

Three main phases of cellular respiration

1. Glycolysis (in the cytoplasm) 2. Pyruvate oxidation and the Krebs cycle (in the mitochondrial matrix) 3. Oxidative phosphorylation (electron transport chain and chemiosmosis in the inner mitochondrial membrane).

Role of NADH and FADH₂ in cellular respiration

NADH and FADH₂ are electron carriers that donate electrons to the electron transport chain (ETC) during oxidative phosphorylation. This process generates a proton gradient used to produce ATP.

Difference between aerobic and anaerobic respiration

Aerobic respiration requires oxygen as the final electron acceptor in the ETC. Anaerobic respiration uses an alternative electron acceptor (e.g., sulfate or nitrate) when oxygen is absent. Fermentation occurs when no electron acceptor is available, and it regenerates NAD⁺ for glycolysis.

Theoretical ATP yield from one glucose molecule in aerobic respiration

Glycolysis: 2 ATP (net) + 2 NADH; Pyruvate oxidation: 2 NADH; Krebs cycle: 2 ATP (GTP) + 6 NADH + 2 FADH₂; Oxidative phosphorylation: ~2.5 ATP per NADH and ~1.5 ATP per FADH₂; Total: ~30-32 ATP per glucose molecule.

Chargaff's rules

The amount of adenine (A) equals thymine (T), and the amount of guanine (G) equals cytosine (C). The ratio of (A+T) to (G+C) varies between species.

Structure of DNA

DNA is a double helix with two antiparallel strands. The backbone is made of sugar-phosphate groups, and the rungs are nitrogenous bases (A-T, C-G) held together by hydrogen bonds.

Role of DNA polymerase in replication

DNA polymerase synthesizes new DNA strands by adding nucleotides in the 5' to 3' direction. It requires a primer with a free 3'-OH group to start synthesis.

Difference between leading and lagging strands

Leading strand: Synthesized continuously in the 5' to 3' direction toward the replication fork. Lagging strand: Synthesized discontinuously in short Okazaki fragments away from the replication fork.

Function of DNA ligase

DNA ligase seals nicks in the DNA backbone by forming phosphodiester bonds between Okazaki fragments on the lagging strand.

Central dogma of molecular biology

The flow of genetic information: DNA → RNA → Protein.

Three main types of RNA and their functions

1. mRNA (messenger RNA): Carries genetic information from DNA to the ribosome for protein synthesis. 2. tRNA (transfer RNA): Brings amino acids to the ribosome during translation. 3. rRNA (ribosomal RNA): Forms the core of the ribosome and catalyzes protein synthesis.

tRNA (transfer RNA)

Brings amino acids to the ribosome during translation.

rRNA (ribosomal RNA)

Forms the core of the ribosome and catalyzes protein synthesis.

RNA polymerase

Synthesizes RNA from a DNA template. It does not require a primer and adds nucleotides in the 5' to 3' direction.

Introns

Non-coding regions of a gene that are removed during RNA splicing.

Exons

Coding regions of a gene that are expressed in the final mRNA.

Genetic code

The set of rules by which mRNA sequences are translated into amino acids.

Degenerate

Refers to the genetic code being degenerate because multiple codons can code for the same amino acid (e.g., 6 codons for leucine).

Role of tRNA in translation

tRNA molecules carry specific amino acids to the ribosome. They have an anticodon that base-pairs with the mRNA codon, ensuring the correct amino acid is added to the growing polypeptide chain.

Function of the ribosome in translation

The ribosome is the site of protein synthesis. It facilitates the binding of mRNA and tRNA and catalyzes the formation of peptide bonds between amino acids.

Shine-Dalgarno sequence

A ribosomal binding site in bacterial mRNA that aligns the initiator codon (AUG) with the initiator tRNA during translation initiation.

Alternative splicing

Allows a single gene to produce multiple proteins by including or excluding different exons during mRNA processing.

Steps of translation

1. Initiation: The ribosome assembles around the mRNA, and the initiator tRNA binds to the start codon (AUG). 2. Elongation: Amino acids are added to the growing polypeptide chain as the ribosome moves along the mRNA. 3. Termination: A stop codon (UAA, UAG, or UGA) signals the end of translation, and the polypeptide is released.

Prokaryotic transcription and translation

In prokaryotes, transcription and translation occur simultaneously in the cytoplasm.

Eukaryotic transcription and translation

In eukaryotes, transcription occurs in the nucleus, and translation occurs in the cytoplasm after mRNA processing.

5' cap in eukaryotic mRNA

Protects mRNA from degradation and helps initiate translation.

Poly-A tail in eukaryotic mRNA

Stabilizes mRNA and aids in export from the nucleus.

End replication problem

Occurs because DNA polymerase cannot fully replicate the ends of linear chromosomes.

Telomerase

Adds repetitive sequences to the ends of chromosomes, solving the end replication problem.

Histones

Proteins that help package DNA into nucleosomes, which fold into chromatin fibers.

Euchromatin

Loosely packed chromatin that is transcriptionally active.

Heterochromatin

Tightly packed chromatin that is transcriptionally inactive.

Glycolysis

A metabolic pathway that converts glucose into pyruvate, producing ATP and NADH.

Krebs cycle

A series of chemical reactions used by all aerobic organisms to generate energy through the oxidation of acetyl-CoA.

Oxidative phosphorylation

The process by which ATP is produced using the energy derived from the electron transport chain.

DNA polymerase

An enzyme that synthesizes DNA molecules from nucleotides, the building blocks of DNA.

Helicase

An enzyme that unwinds the DNA double helix during DNA replication.

Ligase

An enzyme that joins two DNA strands together by forming a phosphodiester bond.

mRNA

Messenger RNA, a type of RNA that conveys genetic information from DNA to the ribosome.

tRNA

Transfer RNA, a type of RNA that helps decode a messenger RNA sequence into a protein.

rRNA

Ribosomal RNA, a component of the ribosome that helps in protein synthesis.

Codon

A sequence of three nucleotides in mRNA that corresponds to a specific amino acid.

Anticodon

A sequence of three nucleotides in tRNA that pairs with the corresponding codon in mRNA.

Genetic code

The set of rules by which information encoded in genetic material is translated into proteins.

Transcription

The process of copying a segment of DNA into RNA.

Translation

The process by which a protein is synthesized from the mRNA sequence.

Splicing

The process of removing introns from pre-mRNA and joining exons together.

Histones

Proteins that package and order DNA into structural units called nucleosomes.

Nucleosomes

The basic unit of DNA packaging, consisting of a segment of DNA wound around a core of histone proteins.

Chromatin

The complex of DNA and proteins that forms chromosomes within the nucleus of eukaryotic cells.

Feedback inhibition

A regulatory mechanism in which the end product of a process inhibits an earlier step.

Lactate

A byproduct of anaerobic metabolism, produced from pyruvate in muscle cells.

Fermentation

A metabolic process that converts sugar to acids, gases, or alcohol in the absence of oxygen.

Electron transport chain (ETC)

A series of protein complexes and other molecules that transfer electrons through a membrane to create a proton gradient.

3' to 5' exonuclease activity

The ability of DNA polymerase to remove mismatched nucleotides from the newly synthesized DNA strand.

Topoisomerases

Enzymes that relieve the strain of supercoiling in DNA during replication.

RNA primers

Short strands of RNA that provide a starting point for DNA synthesis.

Promoter region

A region of DNA that initiates transcription of a particular gene.

Alternative splicing

A process that allows a single gene to code for multiple proteins by varying the combination of exons included in the final mRNA.

Stop codons

Nucleotide triplets in mRNA that signal the termination of translation.

Polypeptide

A chain of amino acids linked by peptide bonds, which folds into a functional protein.

Mutation from UAC to UAG

UAC codes for tyrosine, while UAG is a stop codon. The mutation would cause premature termination of translation, resulting in a truncated, nonfunctional protein.

Mutation in DNA ligase gene

DNA ligase seals nicks in the DNA backbone. Without functional ligase, Okazaki fragments on the lagging strand would not be joined, leading to incomplete DNA replication and potential cell death.

Eukaryotic mRNA lacking 5' cap

The mRNA would not be recognized by the ribosome, leading to a failure in translation initiation. Additionally, the mRNA would be more susceptible to degradation by nucleases.

Genome size of 10,000 base pairs and 20 genes

The organism is likely a prokaryote (e.g., a bacterium) because it has a small genome size and a high gene density, typical of simpler organisms.

Defect in telomerase enzyme

Without telomerase, the telomeres at the ends of chromosomes would shorten with each cell division, eventually leading to chromosome instability, cellular aging, and apoptosis.

Mutation in tRNA synthetase gene

The specific amino acid would not be attached to its corresponding tRNA, leading to incomplete or incorrect protein synthesis and potentially nonfunctional proteins.

Eukaryotic gene with 5 exons and 4 introns

The number of possible proteins depends on which exons are included or excluded. For 5 exons, the number of combinations is 2^5 = 32, but not all combinations may be functional.

Antibiotic inhibiting 30S ribosomal subunit

The antibiotic would prevent the formation of the initiation complex, blocking translation and halting protein synthesis, ultimately killing the bacterial cell.

DNA sequence with 30% adenine (A)

Adenine (A) = 30%, Thymine (T) = 30% (since A pairs with T), Cytosine (C) = 20%, Guanine (G) = 20% (since C pairs with G).

Experiment to determine aerobic or anaerobic respiration

Grow the organism in the presence and absence of oxygen. Measure ATP production, oxygen consumption, and the presence of byproducts (e.g., CO₂ for aerobic, ethanol or lactate for anaerobic). If ATP production is higher in the presence of oxygen, the organism uses aerobic respiration.

Identifying promoter region in bacterial genome

Use bioinformatics tools to search for conserved sequences (e.g., -10 and -35 regions). Perform a reporter gene assay by cloning potential promoter regions upstream of a gene like GFP and measuring expression.

Determining mutation effect in intron

Isolate mRNA from the cell and perform RT-PCR to amplify the gene. Sequence the cDNA to check for abnormal splicing patterns or retention of introns.